February 27th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in gut microbiomes, I recomment taking a look at the preprint by Weiss and collaborator. In this study, they explore bacteria-bacteria interactions, bacterial growth and metabolic interactions in a synthetic bacterial community: the Oligo-Mouse-Microbiota, which is increasingly used as model system in gut microbiome research.

Additionally, anyone interested in microbiome-based forensic tools should read the study from Sang You and collaborators.  They compared the composition of microbial communities in blood spot surfaces placed in different environments sampled across seasons and time points, in order to evaluate the environmental factors leading to variation in these microbial communities.

Today’s non-microbiology pick is a fascinating study looking at the prevalence of COVID-19 related misinformation among the Yemeni population and its association with vaccine acceptance and perceptions. From this study, the authors recommend the deployment of awareness campaigns to decrease misinformation before initiating any mass vaccination in Yemen.

Have a great Weekend!

Human gut microbiome

Review: The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling – Gangadoo et al. – International Journal of Molecular Sciences

Preprint: Exploring the interaction network of a synthetic gut bacterial community – Weiss et al. – BioRxiV

Animal experiments

Environmental concentrations of antibiotics alter the zebrafish gut microbiome structure and potential functions – Rehman Kayani et al. – Environmental Pollution

Fish farm effluents as a source of antibiotic resistance gene dissemination on Jeju Island, South Korea – Jo et al. – Environmental Pollution

Influence of environmental factors and bacterial community diversity in pond water on health of Chinese perch through Gut Microbiota change – Li et al. – Aquaculture Reports

Preprint: The diversity, composition, and metabolic pathways of archaea in pigs – Deng et al. – Preprints

Animal microbiome

Preprint: Stony Coral Tissue Loss Disease biomarker bacteria identified in corals and overlying waters using a rapid field-based sequencing approach – Becker et al. – bioRxiV

Built environment

Microbial analyses of blood spot surfaces collected from a laboratory and the bathroom of a female single-person household under different environmental conditions – Sang You et al – FEMS Microbiology letters

Phages and viruses

Opinion paper: Rapid emergence of virus–host mutualism under stress – Dolja – PNAS

Patterns of virus growth across the diversity of life – Jin and Yin – Integrative biology


Standard Bacteriophage Purification Procedures Cause Loss in Numbers and Activity – Carroll-Portillo et al. – Viruses

My non-microbiology picks

Preprint: Misinformation, Perceptions Towards COVID-19 and Willingness to be Vaccinated: A Population-Based Survey in Yemen – Naoras Bitar et al. – BioRxiV

February 23, 2021

Greetings from Pittsburgh!

Today’s digest is heavy on plant and soil-associated research. It includes a review on the use of metagenomics in soil ecology research, original research focused on the microbiome of plants growing in a Sandhills ecosystem, as well as articles focused on the soil-associated microorganisms Marinobacter caseinilyticus sp. and Dickeya sp. This digest also features several articles focused on extremophiles found in permafrost, the South Pole, and a Mars-like environment! Finally, I also wanted to highlight an Q&A with Dr. Kizzmekia Corbett, an immunologist at the National Institute of Health and one of the designers of the Moderna COVID-19 vaccine.

Events and jobs

Black in Microbiology is now also the Black Microbiologists Association. If you’re interested in joining or learning more information, check out their webpage for details!

General microbiome

Biochemical characterization of a low salt-adapted extracellular protease from the extremely halophilic archaeon Halococcus salifodinae – Hou et al. – International Journal of Biological Macromolecules

Identification and characterization of a metal-resistant Acidithiobacillus ferrooxidans as important potential application for bioleaching – Tavakoli et al. – Biologia

Human vaginal microbiome

Review: Lactic acid-containing products for bacterial vaginosis and their impact on the vaginal microbiota: A systematic review — Plummer et al. – PLOS One

Human gut microbiome

Effects of colon-targeted vitamins on the composition and metabolic activity of the human gut microbiome– a pilot study – Pham et al. – Gut Microbes

Animal experiments

Co-infecting pathogen lineages have additive effects on host bacterial communities – Medina et al. – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Aggregate-related changes in living microbial biomass and microbial necromass associated with different fertilization patterns of greenhouse vegetable soils – Luan et al. – European Journal of Soil Biology

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem – Lopes et al. – FEMS Microbiology Ecology

Marinobacter caseinilyticus sp. nov., isolated from saline soil – Nie et al. – Current Microbiology

Genomic diversity and organization of complex polysaccharide biosynthesis clusters in the genus Dickeya – Ranjan et al. – PLOS One

Review: Metabarcoding and Metagenomics in Soil Ecology Research: Achievements, Challenges, and Prospects – Semenov – Biology Bulletin Reviews

A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin – Shiozaki et al. – PLOS One

Water and extremophile microbiome

Are permafrost microorganisms as old as permafrost? – Abramov et al. – FEMS Microbiology Ecology

Cultivation and characterization of snowbound microorganisms from the South Pole – Hayward et al. – Extremophiles

Survival of desert algae Chlorella exposed to Mars-like near space environment – Wang et al. – Life Sciences in Space Research

Microbes in the news

This COVID-vaccine designer is tackling vaccine hesitancy — in churches and on Twitter – Subbaraman – Nature

Januar 04, 2021

Good morning and happy new year! The first post in 2021 is rather short and covers gut microbiota and cancer, FMT, gut microbiota in calves and microbiome/archeaome of two wild animal species.

Human gut microbiome

Dysbiosis of gut microbiota in patients with esophageal cancer – Deng et al. – Microbial Pathogenesis

[REVIEW]Immunotherapy in Solid Tumors and Gut Microbiota: The Correlation—A Special Reference to Colorectal Cancer – Koulouridi et al. – Cancers

Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry – Kelly et al. – Gastroenterology

Fecal microbiota transplantation for graft-versus-host disease in children and adults: methods, clinical effects, safety – Goloshchapov et al. – Therapeutic archive (Article in Russian)

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Analysis of the developing gut microbiota in young dairy calves—impact of colostrum microbiota and gut disturbances – Hang, Wredle & Dicksved – Tropical Animal Health and Production

Animal microbiome (for animals in the wild)

Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemys scripta) – Parks, Kedy & Skalla – PLOS One

Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte – Polonia et al. – Antonie van Leeuwenhoek Journal of Microbiology

December 31, 2020

General microbiome

Review: Brain-gut axis: From the conditioned reflex to the microbiota-gut-brain communication system – Klara Gyires – Integrative Physiology

Human skin microbiome

Microbiological profile of diabetic foot ulcers in Kuwait – Asma Alhubail – PLOS ONE

Human respiratory microbiome

The airways microbiome of individuals with asthma treated with high and low doses of inhaled corticosteroids – Matthew J Martin – PLOS ONE

Human gut microbiome

The beneficial or detrimental fluoride to gut microbiota depends on its dosages – Guijie Chen – Ecotoxicology and Environmental Safety

Review: Synthetic Gut Microbiome: Advances and Challenges – Humphrey A. Mabwi – Computational and Structural Biotechnology Journal

Review: Microbiota-Gut-Brain Axis as a Regulator of Reward Process – Rubén García-Cabrerizo – Journal of Neurochemistry

Review: Modulatory effects of gut microbiome in cancer immunotherapy: A novel paradigm for blockade of immune checkpoint inhibitors – Sama Rezasoltani – Cancer Medicine

Animal experiments

Effects of heat-killed Enterococcus faecalis T-110 supplementation on gut immunity, gut flora, and intestinal infection in naturally aged hamsters – Takio Inatomi – PLOS ONE

Nasal Tissue Extraction Is Essential for Characterization of the Murine Upper Respiratory Tract Microbiota – L Patrick Schenck – mSphere

Animal microbiome

Review: Gut microbiota of animals living in polluted environments are a potential resource of anticancer molecules – Morhanavallee Soopramanien – Journal of Applied Microbiology

Plant, root, and soil microbiome

Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats  – Martino Adamo – PLOS ONE

Changes in microbial communities at different soil depths through the first rainy season following severe wildfire in North China artificial Pinus tabulaeformis forest – Qianqian Qin – Journal of Environment Management

Shifts in a Phenanthrene-Degrading Microbial Community are Driven by Carbohydrate Metabolism Selection in a Ryegrass Rhizosphere – Longfei Jiang – ACS

Forest gaps mediate the structure and function of the soil microbial community in a Castanopsis kawakamii forest – Xuelin Wang – Ecological Indicators

Review: Herbicide bioremediation: from strains to bacterial communities – Marcos Pileggi – Heliyon

Spatial scale structure soil bacterial communities across an Arctic landscape – Lucie A Malard – Applied and Environmental Microbiology

Metagenomic Analysis of Rhizosphere Bacteria in Desert Plant Calotropis procera – Ahmed M Ramadan

Water and extremophile microbiome

Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte – Ana Rita Moura Polónia – Antonie van Leeuwenhoek

Preprint: Novel integrative elements and genomic plasticity in ocean ecosystems – Thomas Hackl – bioRxiv

Food microbiology

The diversity of microbial communities in Chinese milk fan and their effects on volatile organic compound profiles – Chen Chen – Journal of Dairy Science

Characterizing Relationship of Microbial Community in Xiaoqu and Volatiles of Light-aroma-type Xiaoqu Baijiu – Zhe Wang – Food Science and Technology Research

Virus and phages

Acquisition, prevalence and clearance of type-specific human papillomavirus infections in young sexually active Indian women: A community-based multicentric cohort study – Richard Muwonge – PLOS ONE


Informed sequential pooling approach to detect SARS-CoV-2 infection – Renato Millioni – PLOS ONE

Thesis: Statistical Methods for Longitudinal Data Analysis and Reproducible Feature Selection in – Lingjing Jiang – UC San Diego Electronic Theses and Dissertations

MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences – Yue Xing – Frontiers in Microbiology

Microbes and evolution

Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history – Eva Brons – PLOS BIOLOGY

The role of Ulva fasciata in the evolution of the microbial community and antibiotic resistance genes in maricultural sediments – Yuqin Luo – Marine Pollution Bulletin

Preprint: The Diversity and Evolution of Microbial Dissimilatory Phosphite Oxidation – Sophia D Ewens – bioRxiv

Microbes in the news

Synthetic Biologics Inc. (SYN) Soars 5.43% on December 25 – equities.com

The Brain, Gut and Consciousness: Microbiology of Our Mind – Inquiries Journal

Non-microbiology pick

Preprint: National Institutes of Health Institute and Center Award Rates and Funding Disparities – Michael S Lauer – bioRxiv

Communicating risk in human-wildlife interactions: How stories and images move minds – Sarah K Guenther – PLOS ONE

November 12, 2020

Good morning! There’s a really exciting collection of papers to share with you this morning. Among them, a study of gut archaea across multiple host domains, a link between F. nucleatum and esophageal cancer, and two new databases of shotgun metagenomic data. (There’s also a fun paper about environmental transmission of microbes aboard the International Space Station.)

General microbiome

Preprint – Strong influence of vertebrate host phylogeny on gut archaeal diversity, Nicholas D Youngblut et al., bioRxiv

A genomic catalog of Earth’s microbiomes, Stephen Nayfach et al., Nature Biotechnology

Human vaginal microbiome

Review – Vaginal microbiota and the potential of Lactobacillus derivatives in maintaining vaginal health, Wallace Jeng Yang Chee, Microbial Cell Factories

Human gut microbiome

Preprint – Fusobacterium Nucleatum Predicts a Risk for Esophageal Squamous Cell Carcinoma, Chao Shi et al., Research Square

Preprint – Human reference gut microbiome comprising 5,414 prokaryotic species, including newly assembled genomes from under-represented Asian metagenomes, Kim and Lee et al., bioRxiv

Preprint – Genetic Evidence for Selective Transfer of Microbes Between the International Space Station and an Astronaut, David C. Danko et al., bioRxiv

Review: An infectious diseases perspective on the microbiome and allogeneic stem cell transplant, Olivia C. Smibert et al., Current Opinion in Infectious Diseases

Animal experiments

Preprint – Longitudinal effects of antibiotics and fecal transplant on lemur gut microbiota structure, associations, and resistomes, Sally L. Bornbusch et al., bioRxiv

Pinto beans modulate the gut microbiome, augment MHC II protein, and antimicrobial peptide gene expression in mice fed a normal or western-style diet, Babajide A. Ojo et al., Journal of Nutritional Biochemistry

Preprint – Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents of the Zebrafish Gut, Wesley Loftie-Eaton et al., bioRxiv

Animal microbiome

Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys, Anna J. Jasinska et al., Microbiome

A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo, Narat and Amato et al., Scientific Reports


Preprint – AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities, Almut Heinken et al., bioRxiv


Preprint – Benchmarking DNA isolation kits used in analyses of the urinary microbiome, Lisa Karstens et al., bioRxiv

November 5, 2020

Hello, friends!

I’m an American who grew up in North Carolina, lived in Georgia for many years, and now counts Pennsylvania as home. All of this is to say, I’ve been especially consumed by the US election this morning and so today’s digest is tailor made to distract me for a few hours. It contains a heavy dose of general microbiome, environmental microbiology, and microbial ecology articles. If you need a bigger distraction than usual, I’ve highlighted a few articles that I am particularly looking forward to reading and am using this space as an opportunity to reintroduce myself and share why these articles have peaked my interest.

I completed my PhD research on the cockroach gut microbiome and through this work, I realized how complex microbiome-host-environmental interactions can be. Because of this, my first highlighted article is a review about cockroach-associated microbes. Currently, I work in a national lab studying environmental-associated microbes (and their functional capacity!) in a variety of different energy-associated environments. It’s no wonder I’m excited to read the second highlighted article focused on novel soil microbes found in an abandoned coal mine! I’m also very hungry at the moment, so as soon I read the phrase “smoked cow cheese” I was motivated to explore my cheese drawer as well as think more about microbial food safety and the microbial production of favor compounds. Finally, I love musical theater and science outreach, so I’m delighted to share a mouldy article that combines both passions.

Happy reading, everyone!

General microbiome

Review: The pneumococcal social network – Aggarawal et al. – PLOS Pathogens

Expanding magnetic organelle biogenesis in the domain Bacteria – Lin et al. – Microbiome

Gene duplication drives genome expansion in a major lineage of Thaumarchaeota – Sheridan et al. – Nature Communications

Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress – Yu et al. – Ecotoxicology

Effects of heavy ion particle irradiation on spore germination of Bacillus spp. from extremely hot and cold environments – Zammuto et al. – Life
Human gut microbiome

Gut microbiome

Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging – Sala et al. – PLOS ONE

Implication of gut microbiota in the physiology of rats intermittently exposed to cold and hypobaric hypoxia – Ramos-Romero et al. – PLOS ONE

Animal microbiome

Exploring the resident gut microbiota of stranded odontocetes: high similarities between two dolphin species Tursiops truncatus and Stenella coeruleoalba – Abdelrhman et al. – Journal of the Marine Biological Association of the UK

**Review: Bacteria associated with cockroaches: health risk or biotechnological opportunity? – Guzman & Vilcinskas – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Impact of land uses, drought, flood, wildfire, and cascading events on water quality and microbial communities: A review and analysis – Mishra et al. – Journal of Hydrology

Dams shift microbial community assembly and imprint nitrogen transformation along the Yangtze River – Gao et al. – Water Research

Built environment

**Isolation and characterization of soil bacteria from an abandoned coal mine in southeast Kansas – Bechtold et al. – BioOne Complete

Review: Understanding building-occupant-microbiome interactions toward healthy built environments – Li et al. – Frontiers of Environmental Science & Engineering

Food microbiology

**Microbial quality of smoked cow cheese “Parencia” – Kačániová et al. – Scientific Papers: Animal Science and Biotechnologies

Phages and viruses

Virome of bat guano from nine northern California roosts – Li et al. – Journal of Virology


The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities – Chen et al. – Nucleic Acids Research

PhANNs, a fast and accurate tool and web server to classify phage structural proteins – Cantu et al. – PLOS Computational Biology


Low-cost biofuel-powered autoclaving machine for use in rural health care centres – Ahmed et al. – Journal of Medical Engineering & Technology

**‘The Mould that Changed the World’: Quantitative and qualitative evaluation of children’s knowledge and motivation for behavioural change following participation in an antimicrobial resistance musical – Hall et al. – PLOS ONE

Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes – McClenaghan et al. – PLOS ONE

October 1, 2020

Greetings, friends!

Today’s digest contains a wealth of microbiology articles focused on everything from the dog ear canal microbiome to estuarine methanogen communities. Rather than highlight a specific research article, today I’d like to encourage you to check out this week’s New York Times article profiling the organizers of Black in Micro Week and this commentary published by one of the organizers in mSphere. Black in Micro week began this Monday and programming is scheduled to continue through October 4th. If you missed earlier events, you’re in luck! The organizers have already uploaded videos of all completed events at the Black in Micro youtube channel.



Black in Micro Week is this week (September 28 – October 4th, 2020) on your favorite social media platforms! Check out the Black in Microbiology website for additional information, including a full programming schedule, and follow @BlackinMicro and #BlackinMicro on Twitter and Instagram.

Human respiratory microbiome

Airway microbiota is associated with the severity of non‐CF bronchiectasis – Li et al. – The Clinical Respiratory Journal

Human gut microbiome

Systematic analysis of gut microbiota in pregnant women and its correlations with individual heterogeneity – Yang et al. – npj Biofilms and Microbiomes

Review: Implication of gut microbiota in cardiovascular diseases – Zhou et al. – Oxidative Medicine and Cellular Longevity

Animal experiments

Changes in the ear canal microbiota of dogs with otitis externa – Kasai et al. – Journal of Applied Microbiology

Plant, root, and soil microbiome

Soil borne Fusarium solani exhibited pathogenic effect on tomato cultivars in Nigeria – Abiala et al. – Archives of Phytopatholgy and Plant Protection

A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus – Nelson et al. – The ISME Journal

Successional change of the fungal microbiome pine seedling roots inoculated with Tricholoma matsutake – Park et al. – Frontiers in Microbiology

Review: Arbuscular mycorrhizal fungi: an ecological accelerator of phytoremediation of metal contaminated soils – Tiwari et al. – Archives of Agronomy and Soil Science

Co‐occurrence history increases ecosystem stability and resilience in experimental plant communities – van Moorsel et al. – Ecology

Quantitative estimation of stochastic and deterministic processes for soil prokaryotic community assembly in the Yellow River floodplain – Yu et al. – European Journal of Soil Science

Water and extremophile microbiome

Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre – Allen et al. – Molecular Ecology

An unexpectedly broad thermal and salinity-tolerant estuarine methanogen community – Blake et al. – Microorganisms

Microbial communities responded to tetracyclines and Cu(II) in constructed wetlands microcosms with Myriophyllum aquaticum – Guo et al. – Ecotoxicology and Environmental Safety

Built environment

Microbial community and function in nitrogen transformation of ectopic fermentation bed system for pig manure composting – Chen et al. – Bioresource Technology

Effect of hydrothermal hot-compression method on the antimicrobial performance of green building materials from heterogeneous cellulose wastes – Echeverria et al. – Journal of Cleaner Production

Nitrous oxide emission and microbial community of full-scale anoxic/aerobic membrane bioreactors at low dissolved oxygen setpoints – Wen et al. – Journal of Water Process Engineering

Response of Cyperus involucratus to sulfamethoxazole and ofloxacin-contaminated environments: Growth physiology, transportation, and microbial community – Xu et al. – Ecotoxicology and Environmental Safety

Microbes in the news

Black microbiologists push for visibility amid a pandemic – Wu – New York Times

Science, publishing, and career

Commentary: mSphere of influence: That’s racist—COVID-19, biological determinism, and the limits of hypotheses – Taylor – mSphere

September 8, 2020

Greetings, friends!

Today’s digest is a very heavy grab bag of articles! Included are many reviews on everything from the microbiome in forensic science to the gut-lung axis. Also included are original research articles focused on a variety of subjects including microplastics, extremophiles, and the bicycle microbiome! Finally, for those of you looking for practical advice, I’ve highlighted an article focused on best practices for writing genome announcements.

Happy reading!

General microbiome

Manipulating denitrifying sulfide removal of Pseudomonas sp. C27 with nitrite as sole nitrogen source: Shotgun proteomics analysis – Guo et al. – Bioresource Technology

Pseudomonas aeruginosa – Candida interplay: Effect on in vitro antibiotic susceptibility of Pseudomonas aeruginosa when grown in the presence Candida culture – Mcllroy et al. – British Journal of Biomedical Science

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates – Nouws et al. – Scientific Reports

Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community – Padfield et al. – The ISME Journal

Biomass-degrading glycoside hydrolases of archaeal origin – Suleiman et al. – Biotechnology for Biofuels

Mining for novel antibiotics in the age of antimicrobial resistance – Udaondo and Matilla – Microbial Biotechology

Multi-site human microbiome

Association between the microbiomes of tonsil and saliva samples isolated from pediatric patients subjected to tonsillectomy for the treatment of tonsillar hyperplasia – Choi et al. – Experimental & Molecular Medicine

Review: The impact of the human microbiome in forensic sciences: A systematic review – García et al. – Applied and Enviornmental Microbiology

Human respiratory microbiome

Review: The evolving role of the lung microbiome in pulmonary fibrosis – Lipinski et al. – Lung Cellular and Molecular Physiology

Review: Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis – Willis et al. – Lung Cellcular and Molecular Physiology

Human gut microbiome

Altered gut microbiota correlated with systemic inflammation in children with Kawasaki disease – Chen et al. – Scientific Reports

Review: Gut microbiota in human metabolic health and disease – Fan and Pedersen – Nature Reviews Microbiology

Lactose-reduced infant formula with added corn syrup solids is associated with a distinct gut microbiota in Hispanic infants – Jones et al. – Gut Microbes

Animal experiments

Gut bacterial communities and their contribution to performance of specialist Altica flea beetles – Wei et al. – Microbial Ecology

Dynamic changes of gut microbiota of discus fish (Symphysodon haraldi) at different feeding stages – Zhang et al. – Aquaculture

Plant, root, and soil microbiome

Diversity of cultivable microbes from soil of the Fildes Peninsula, Antarctica, and their potential application – Cong et al. – Frontiers in Microbiology

Structural and functional microbial diversity of sandy soil under cropland and grassland – Frąc et al. – PeerJ

Microbiome–environment interactions in antimony-contaminated rice paddies and the correlation of core microbiome with arsenic and antimony contamination – Li et al. – Chemosphere

Review: Implications of endophytic microbiota in Camellia Sinensis: A review on current understanding and future insights – Xie et al. – Bioengineered

Characterizing the nectar microbiome of the non-native tropical milkweed, Asclepias curassavica, in an urban environment – Warren et al. – PLOS ONE

Water and extremophile microbiome

Prokaryotic diversity in stream sediments affected by acid mine drainage – Carlier et al. – Extremophiles

Combination of genetic tools to discern Bacillus species isolated from hot springs in South Africa – Jardine and Ubomba-Jaswa – African Journal of Mirobiology Research

Bioleaching of pyritic coal wastes: bioprospecting and efficiency of selected consortia – Joulian et al. – Research in Microbiology

Genotypic and phylogenetic diversity of new isolates of terrestrial Xanthophyceae (Stramenopiles) from maritime sandy habitats – Rybalka et al. – Phycologia

Paucihalobacter ruber gen. nov., sp. nov., isolated from a haloalkaline lake sediment sample – Wu et al. – Microbiology Society

Comparative analysis of bacterial diversity and community structure in the rhizosphere and root endosphere of two halophytes, Salicornia europaea and Glaux maritima, collected from two brackish lakes in Japan – Yamamoto et al. – Microbes and Environments

Fungal diversity in deep-sea sediments from Magellan seamounts environment of the western Pacific revealed by high-throughput Illumina sequencing – Yang et al. – Journal of Microbiology

Effect of Ferrous Iron Addition on Ammonium Nitrogen Removal and Microbial Communities in Horizontal Subsurface Flow Constructed Wetlands – Zhang et al. – Wetlands

Built environment

Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment – Lin et al. – Proceedings of the Royal Society B

Shared bicycle microbial community: a potential antibiotic-resistant bacteria warehouse – Wu et al. – Folia Microbiologica

Microbial carrying capacity and carbon biomass of plastic marine debris – Zhao et al. – The ISME Journal

Food microbiology

Proteolysis, lipolysis, texture and sensory properties of cheese ripened by Monascus fumeus – Xia et al. – Food Research International


Announcement: Best practices for successfully writing and publishing a genome announcement in microbiology resource announcements – Hotopp et al. – Microbiology Resource Announcements


Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities – Mooshammer et al. – The ISME Journal

August 28, 2020


Today’s microbiome digest has something for everyone. We have several articles focused on the human microbiome, a few animal studies, and quite a few articles focused on environmental bacteria found in soil, water, and even a cave! I want to highlight one article focused on the impact of spatial proximity on territory among bacteria. Although the article specifically focuses on skin bacteria, it’s relevant to anyone studying microbial communities!


General microbiome

Horizontal transmission and recombination maintain forever young bacterial symbiont genomes – Russel et al. – PLOS GENETICS

Human skin microbiome

Impact of spatial proximity on territoriality among human skin bacteria – Hernandez-Valdes et al. – npj BIofilms and Microbiomes

Human gut microbiome

Gut microbiota and dysbiosis in Alzheimer’s disease: Implications for pathogenesis and treatment – Liu et al. – Molecular Neurobiology

Animal experiments

Caecal microbiota compositions from 7-day-old chicks reared in high-performance and low-performance industrial farms and systematic culturomics to select strains with anti-Campylobacter activity – Duquenoy et al. – PLOS ONE

Effect of FHA and Prn on Bordetella pertussis colonization of mice is dependent on vaccine type and anatomical site – Zeddeman et al. – PLOS ONE

Animal microbiome

Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America – Milovic et al. – PLOS ONE

Plant, root, and soil microbiome

Simple kinetics, assay, and trends for soil microbial catalases – Chabot et al. – Analytical Biochemistry

Sustaining the growth of Pinaceae trees under nutrient-limited edaphic conditions via plant-beneficial bacteria – Puri et al. – PLOS ONE

Soil properties, bacterial and fungal community compositions and the key factors after 5-year continuous monocropping of three minor crops – Yang et al. – PLOS ONE

Water and extremophile microbiome

Oleaginous potential of indigenously isolated fresh water microalgae for biofuel production – Saraf & Dutt – International Journal of Sustainable Energy

Bacteria and archaea communities in Cerrado natural pond sediments – Silveira et al. – Microbiology of Aquatic Systems

The microbial community of a biofilm lining the wall of a pristine cave in Western New Guinea – Turrini et al. – Microbiological Research

On microbial community of Pyropia haitanensis by metagenomic analysis – Wang et al. – Journal of Oceanology and Limnology

August 19, 2020


Today’s digest is heavy on environmental microbiology with topics ranging from marine microplastics to carbon budgets to kitchen waste. I want to especially highlight a study that examines the phyllosphere of the mānuka. They found that the mānuka, or tea tree, has a stable core microbiome and variation in the non-core taxa is explained by biogeographical patterns.


Events and jobs

Virtual Microbiome Bioinformatics Qiime2 Workshop – October 5-9, 2020

General microbiome

Opinion: Oceanic hitchhikers – Assessing pathogen risks from marine microplastic – Bowley et al. – Trends in Microbiology

Multi-site human microbiome

Analysis of the composition and functions of the microbiome in diabetic foot osteomyelitis based on 16S rRNA and metagenome sequencing technology – Mengchen et al. – Diabetes

Animal experiments

Developmental stage-associated microbiota profile of the peach fruit fly, Bactrocera zonata (Diptera: Tephritidae) and their functional prediction using 16S rRNA gene metabarcoding sequencing – Naaz et al. – 3 Biotech

Plant, root, and soil microbiome

A core phyllosphere microbiome exists across distant populations of a tree species indigenous to New Zealand – Noble et al. – PLOS One

Water and extremophile microbiome

Carbon budgets for soil and plants respond to long-term warming in an Alaskan boreal forest – Alster et al. – Biogeochemistry

First insights to the microbial communities in the plant process water of the multi-metal Kevitsa mine – Bomberg et al. – Research in Microbiology

Halomicroarcula amylolytica sp. nov., a novel halophilic archaeon isolated from a salt mine – Chen et al. – International Journal of Systematic and Evolutionary Microbiology

Spatial patterns of microbial communities across surface waters of the Great Barrier Reef – Frade et al. – Communications Biology

Isolation and characterization of a novel acidophilic zero-valent sulfur- and ferric iron-respiring Firmicute – Holanda and Johnson – Research and Microbiology

Combining physicochemical properties and microbiome data to evaluate the water quality of South African drinking water production plants – Maguvu et al. – PLOS One

Transient dynamics of archaea and bacteria in sediments and brine Across a salinity gradient in a solar saltern of Goa, India – Mani et al. – Frontiers in Microbiology

Diversity and distribution of cultivable fungi present in acid sulphate soils in chronosequence under para-periglacial conditions in King George Island, Antarctica – Porto et al. – Extremophiles

Investigation of the ecological roles of putative keystone taxa during tailing revegetation – Sun et al. – Environmental Science & Technology

Geochemistry and microbiology predict environmental niches with conditions favoring potential microbial activity in the Bakken shale – Tinker et al. – Frontiers in Microbiology

Spatial patterns of selenium and profiling of Se-tolerant Bacillus strains in Shiwalik foot-hills – Tiwana et al. – Geomicrobiology Journal

Bacterial laccase of Anoxybacillus ayderensis SK3-4 from hot springs showing potential for industrial dye decolorization – Wang et al. – Annals of Microbiology

Built environment

Comparison of microbial communities during anaerobic digestion of kitchen waste: Effect of substrate sources and temperatures – Jiang et al. – Bioresource Technology